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Global Database (global + database)
Selected AbstractsInferring historical introduction pathways with mitochondrial DNA: the case of introduced Argentine ants (Linepithema humile) into New ZealandDIVERSITY AND DISTRIBUTIONS, Issue 5 2007Steve E. Corin ABSTRACT The threat imposed by invasive species and difficulties associated with control and management places more impetus on trying to prevent their introduction. The identification of introduction pathways is a vital component towards this goal. In this study, we use a genetic marker-based approach to retrospectively investigate the pathway of origin of the invasive Argentine ant (Linepithema humile) into New Zealand. We intensively sample the mitochondrial gene cytochrome b, from the entire known range of Argentine ants in New Zealand. No genetic variation was found in New Zealand. In order to identify likely introduction pathways, we use two alternative genetic analyses and suggest that a tcs approach that collapses identical haplotypes and calculates the probability of parsimony is superior to standard phylogenetic tree-building algorithms. A minimum spanning network allowed relationships to be examined among sequences collated from previous international studies. The cytochrome b sequence, when compared to a global database, matched that from an Australian population. That Australia is the potential source of Argentine ants is in agreement with the New Zealand interception record, as goods from Australia have the highest number of interception records of Argentine ants. Our approach can easily be duplicated for other organisms and the methodology can be more widely applied to help aid further efforts to identify the routes of transmission for other invasive species and allow us to efficiently direct our biosecurity monitoring effort. [source] Investigating Burkholderia cepacia complex populations recovered from Italian maize rhizosphere by multilocus sequence typingENVIRONMENTAL MICROBIOLOGY, Issue 7 2007Claudia Dalmastri Summary The Burkholderia cepacia complex (BCC) comprises at least nine closely related species of abundant environmental microorganisms. Some of these species are highly spread in the rhizosphere of several crop plants, particularly of maize; additionally, as opportunistic pathogens, strains of the BCC are capable of colonizing humans. We have developed and validated a multilocus sequence typing (MLST) scheme for the BCC. Although widely applied to understand the epidemiology of bacterial pathogens, MLST has seen limited application to the population analysis of species residing in the natural environment; we describe its novel application to BCC populations within maize rhizospheres. 115 BCC isolates were recovered from the roots of different maize cultivars from three different Italian regions over a 9-year period (1994,2002). A total of 44 sequence types (STs) were found of which 41 were novel when compared with existing MLST data which encompassed a global database of 1000 clinical and environmental strains representing nearly 400 STs. In this study of rhizosphere isolates approximately 2.5 isolates per ST was found, comparable to that found for the whole BCC population. Multilocus sequence typing also resolved inaccuracies associated with previous identification of the maize isolates based on recA gene restriction fragment length polymorphims and species-specific polymerase chain reaction. The 115 maize isolates comprised the following BCC species groups, B. ambifaria (39%), BCC6 (29%), BCC5 (10%), B. pyrrocinia (8%), B. cenocepacia IIIB (7%) and B. cepacia (6%), with BCC5 and BCC6 potentially constituting novel species groups within the complex. Closely related clonal complexes of strains were identified within B. cepacia, B. cenocepacia IIIB, BCC5 and BCC6, with one of the BCC5 clonal complexes being distributed across all three sampling sites. Overall, our analysis demonstrates that the maize rhizosphere harbours a massive diversity of novel BCC STs, so that their addition to our global MLST database increased the ST diversity by 10%. [source] Frequent monitoring of temperature: an essential requirement for site selection in bivalve aquaculture in tropical,temperate transition zonesAQUACULTURE RESEARCH, Issue 10 2006Marķa Teresa Sicard Abstract Frequent monitoring of temperature (FMT) for over 1 year at two aquaculture sites in the western Baja California peninsula was analysed in terms of hourly, daily and monthly variability, and with this information, temperature-change indices were calculated. These data were contrasted against a long-term series from a global database (Extended Reconstruction of Sea Surface Temperature (ERSST)) to evaluate whether these could substitute for FMT. The compatibility of species requirements with the thermal conditions was evaluated by comparing the temperature frequency distributions from the two FMTs, with the optimum and lethal temperature information available on five bivalve species of aquacultural interest. We concluded that there was no correlation between ERSST and FMT because the former underestimates the amplitude of real temperature fluctuations and exhibits a different pattern of variation during the year. Therefore, FMT was needed for a correct selection of an aquaculture site for bivalves. The FMT indicated high temperature variability at both sites studied on different time scales, with the site located at lower latitude (Rancho Bueno) warmer and with a higher variability than Laguna Manuela. Contrasting these results with optimum and lethal temperature values of bivalve species, it was possible to find the ideal site, for temperature, for culturing the species, taking into account the variability associated with large-scale phenomena. [source] MolProbity: all-atom structure validation for macromolecular crystallographyACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2010Vincent B. Chen MolProbity is a structure-validation web service that provides broad-spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It relies heavily on the power and sensitivity provided by optimized hydrogen placement and all-atom contact analysis, complemented by updated versions of covalent-geometry and torsion-angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X-ray crystallography provides a wealth of biologically important molecular data in the form of atomic three-dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high-resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database. [source] Burden of disease attributable to selected environmental factors and injury among children and adolescents in EuropeCHILD: CARE, HEALTH AND DEVELOPMENT, Issue 6 2004Richard Reading Burden of disease attributable to selected environmental factors and injury among children and adolescents in Europe . ValentF, LittleD, BertolliniR, NemerLE, BarboneF & TamburliniG . ( 2004 ) Lancet , 363 , 2032 , 2039 . Background Environmental exposures contribute to the global burden of disease. We have estimated the burden of disease attributable to outdoor and indoor air pollution, inadequate water and sanitation, lead exposure, and injury among European children and adolescents. Methods Published studies and reports from international agencies were reviewed for calculation of risk-factor exposure in Europe. Disability-adjusted life years (DALYs) or deaths attributable to each factor, or both, were estimated by application of the potential impact fraction to the estimates of mortality and burden of disease from the WHO global database of burden of disease. Findings Among children aged 0,4 years, between 1.8% and 6.4% of deaths from all causes were attributable to outdoor air pollution; acute lower-respiratory-tract infections attributable to indoor air pollution accounted for 4.6% of all deaths and 3.1% of DALYs; and mild mental retardation resulting from lead exposure accounted for 4.4% of DALYs. In the age-group 0,14 years, diarrhoea attributable to inadequate water and sanitation accounted for 5.3% of deaths and 3.5% of DALYs. In the age-group 0,19 years, injuries were the cause of 22.6% of all deaths and 19.0% of DALYs. The burden of disease was much higher in European subregions B and C than subregion A. There was substantial uncertainty around some of the estimates, especially for outdoor air pollution. Interpretation Large proportions of deaths and DALYs in European children are attributable to outdoor and indoor air pollution, inadequate water and sanitation, lead exposure, and injuries. Interventions aimed at reducing children's exposure to environmental factors and injuries could result in substantial gains. The pronounced differences by subregion and age indicate the need for targeted action. [source] | ||||||||||